Index

A

append_to_run_log() (in module exo2micro.utils)

B

boundary_correlation_coarse() (in module exo2micro.alignment) build_clean_tissue_mask() (in module exo2micro.utils)

build_suffix() (in module exo2micro.defaults) build_task_list() (in module exo2micro.parallel) build_tissue_mask() (in module exo2micro.utils)

C

check_or_raise() (exo2micro.utils.MemoryWatchdog method) checkpoint_exists() (in module exo2micro.utils) classify_raw_files() (in module exo2micro.utils)

clear_run_log() (in module exo2micro.utils) collect_and_snapshot() (exo2micro.utils.MemoryTracker method) compare() (exo2micro.pipeline.SampleDye method) compile_ims_old() (in module exo2micro.legacy)

D

diagnose_raw_layout() (in module exo2micro.utils)

discover_tasks() (in module exo2micro.utils)

E

equalize_pair() (in module exo2micro.utils) estimate_gauss_sigma() (in module exo2micro.utils) estimate_pipeline_memory() (in module exo2micro.utils) estimate_pipeline_output_size() (in module exo2micro.utils) exo2micro.alignment module exo2micro.defaults module exo2micro.legacy module

exo2micro.parallel module exo2micro.pipeline module exo2micro.plotting module exo2micro.utils module

F

filter_nan_gaussian_conserving() (in module exo2micro.utils)

flush() (exo2micro.utils.TeeStdout method) format_bytes() (in module exo2micro.utils)

G

get_available_memory() (in module exo2micro.utils)

get_free_disk_space() (in module exo2micro.utils) get_run_log_path() (in module exo2micro.utils)

I

is_tripped() (exo2micro.utils.MemoryWatchdog method)

L

load_checkpoint() (in module exo2micro.utils)

load_image_pair() (in module exo2micro.utils)

M

make_rgb_overlay() (in module exo2micro.utils) mask_em() (in module exo2micro.legacy) maskandsave() (in module exo2micro.legacy) MemoryTracker (class in exo2micro.utils) MemoryWatchdog (class in exo2micro.utils) module exo2micro.alignment exo2micro.defaults exo2micro.legacy exo2micro.parallel exo2micro.pipeline exo2micro.plotting exo2micro.utils

N

non_default_params() (exo2micro.pipeline.SampleDye method)

normalize_image() (in module exo2micro.utils)

O

optimize_subtraction() (in module exo2micro.legacy)

P

pad_images() (in module exo2micro.utils) params (exo2micro.pipeline.SampleDye property) params_from_suffix() (in module exo2micro.defaults) plot_diff_comparison() (in module exo2micro.legacy) plot_difference_histogram() (in module exo2micro.plotting) plot_difference_image() (in module exo2micro.plotting) plot_excess_heatmap() (in module exo2micro.plotting) plot_fine_alignment() (in module exo2micro.plotting) plot_im() (in module exo2micro.plotting) plot_im_sub() (in module exo2micro.legacy) plot_pre_post_heatmap() (in module exo2micro.plotting) plot_pre_post_histograms() (in module exo2micro.plotting)

plot_ratio_histogram() (in module exo2micro.legacy) plot_ratio_histogram_simple() (in module exo2micro.plotting) plot_registration() (in module exo2micro.plotting) plot_residual_histogram() (in module exo2micro.legacy) plot_signal_scatter() (in module exo2micro.legacy) plot_stretch_comparison() (in module exo2micro.legacy) plot_zoom() (in module exo2micro.plotting) plot_zoom_multi() (in module exo2micro.plotting) plot_zoom_region() (in module exo2micro.legacy) prealign_phase_correlation() (in module exo2micro.alignment) preflight_check() (in module exo2micro.utils) print_summary() (in module exo2micro.parallel) process_one() (in module exo2micro.parallel)

R

read_run_log_tail() (in module exo2micro.utils) refine_icp() (in module exo2micro.alignment) refine_interior_ecc() (in module exo2micro.alignment) refine_interior_sift() (in module exo2micro.alignment) register_highorder() (in module exo2micro.alignment) register_loworder() (in module exo2micro.legacy) reset() (exo2micro.utils.MemoryWatchdog method)

reset_params() (exo2micro.pipeline.SampleDye method) residuals_collapsed() (in module exo2micro.legacy) robust_vmax() (in module exo2micro.utils) run() (exo2micro.pipeline.SampleDye method) run_batch() (in module exo2micro.parallel) run_parallel() (in module exo2micro.parallel) run_serial() (in module exo2micro.parallel) run_subprocess() (in module exo2micro.parallel)

S

SampleDye (class in exo2micro.pipeline) save_checkpoint() (in module exo2micro.utils) set_params() (exo2micro.pipeline.SampleDye method) snapshot() (exo2micro.utils.MemoryTracker method) start() (exo2micro.utils.MemoryWatchdog method)

status() (exo2micro.pipeline.SampleDye method) stop() (exo2micro.utils.MemoryWatchdog method) subtract_median() (in module exo2micro.utils) summary() (exo2micro.utils.MemoryTracker method) survey_raw_channels() (in module exo2micro.utils)

T

TeeStdout (class in exo2micro.utils) tiff_to_fits() (in module exo2micro.utils)

tifffile_save() (in module exo2micro.utils) trim_to_signal() (in module exo2micro.utils)

W

write() (exo2micro.utils.TeeStdout method)